Merge pull request #134 from nf-core/dev

Prepare for bugfix release 1.5.1

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Pull docker image
         run: |
-          docker pull nfcore/mhcquant:dev && docker tag nfcore/mhcquant:dev nfcore/mhcquant:1.5
+          docker pull nfcore/mhcquant:dev && docker tag nfcore/mhcquant:dev nfcore/mhcquant:1.5.1
       - name: Run pipeline with test data
         run: |
           sudo nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT

CHANGELOG.md

@@ -1,5 +1,16 @@
 # nf-core/mhcquant: Changelog
 
+## v1.5.1 nf-core/mhcquat "Flying Fish" - 2020/04/24
+
+### `Fixed`
+
+- set optimal config for cluster execution
+- fix duplication of ids / mixing of channels
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.5 nf-core/mhcquat "Flying Fish" - 2020/04/18
 
 ### `Fixed`

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-mhcquant-1.5 > nf-core-mhcquant-1.5.yml
+RUN conda env export --name nf-core-mhcquant-1.5.1 > nf-core-mhcquant-1.5.1.yml
 
 # Add conda installation dir and thirdparties to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-mhcquant-1.5/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mhcquant-1.5.1/bin:$PATH

conf/base.config

@@ -12,8 +12,8 @@
 process {
 
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-  time = { check_max( 24.h * task.attempt, 'time' ) }
+  memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+  time = { check_max( 2.h * task.attempt, 'time' ) }
 
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
   maxRetries = 1
@@ -28,21 +28,22 @@ process {
   }
   withLabel:process_medium {
     cpus = { check_max( 6 * task.attempt, 'cpus' ) }
-    memory = { check_max( 42.GB * task.attempt, 'memory' ) }
-    time = { check_max( 12.h * task.attempt, 'time' ) }
+    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+    time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withLabel:process_high {
-    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
-    memory = { check_max( 84.GB * task.attempt, 'memory' ) }
-    time = { check_max( 24.h * task.attempt, 'time' ) }
+  withLabel:process_medium_long {
+    cpus = { check_max( 6 * task.attempt, 'cpus' ) }
+    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+    time = { check_max( 8.h * task.attempt, 'time' ) }
   }
-  withLabel:process_long {
-    time = { check_max( 48.h * task.attempt, 'time' ) }
+  withLabel:process_web {
+    time = { check_max( 6.h * task.attempt, 'time' ) }
+    errorStrategy = 'retry'
+    maxRetries = 10
   }
   withName:get_software_versions {
     cache = false
   }
-
 }
 
 params {

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-mhcquant-1.5
+name: nf-core-mhcquant-1.5.1
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -470,6 +470,8 @@ process output_documentation {
 process generate_proteins_from_vcf {
     publishDir "${params.outdir}/"
 
+    label 'process_web'
+
     input:
      set val(Sample), val(id), file(fasta_file_vcf), val(d), file(vcf_file) from input_fasta_vcf.combine(input_vcf, by:1)
 
@@ -557,7 +559,7 @@ process peak_picking {
 process db_search_comet {
     tag "${Sample}"
 
-    label 'process_high'
+    label 'process_medium_long'
 
     input:
      set val(Sample), val(id), val(Condition), file(mzml_file), val(d), file(fasta_decoy) from raws_converted.mix(input_mzmls.mix(input_mzmls_picked)).join(fastafile_decoy_1.mix(input_fasta_1), by:1, remainder:true) 
@@ -603,7 +605,7 @@ process index_peptides {
      set val(Sample), val(id), val(Condition), file(id_file), val(d), file(fasta_decoy) from id_files.join(fastafile_decoy_2.mix(input_fasta_2), by:1)
 
     output:
-     set val("$id"), val("$Sample"), val("$Condition"), file("${Sample}_${Condition}_${id}_idx.idXML") into (id_files_idx, id_files_idx_original, id_files_idx_original_II)
+     set val("$id"), val("$Sample"), val("$Condition"), file("${Sample}_${Condition}_${id}_idx.idXML") into (id_files_idx, id_files_idx_original)
 
     script:
      """
@@ -716,10 +718,13 @@ if(!params.skip_quantification){
     .join(id_files_trafo_II.transpose().flatMap{ it -> [tuple(it[1].baseName.split('_-_')[0].toInteger(), it[0], it[1])]}, by: [0,1])
     .set{joined_trafos_ids}
 
+   id_files_idx_original_II = Channel.empty()
+
 } else {
 
    joined_trafos_mzmls = Channel.empty()
    joined_trafos_ids = Channel.empty()
+   id_files_idx_original_II = id_files_idx_original
 
 }
 /*
@@ -1323,7 +1328,7 @@ process predict_peptides_mhcflurry_class_1 {
 process predict_possible_neoepitopes {
     publishDir "${params.outdir}/"
 
-    label 'process_high'
+    label 'process_web'
 
     input:
      set val(id), val(Sample), val(alleles), file(vcf_file) from neoepitopes_class_1_alleles.join(input_vcf_neoepitope, by:[0,1], remainder:true)
@@ -1348,7 +1353,7 @@ process predict_possible_neoepitopes {
 process predict_possible_class_2_neoepitopes {
     publishDir "${params.outdir}/"
 
-    label 'process_high'
+    label 'process_web'
 
     input:
      set val(id), val(Sample), val(alleles_II), file(vcf_file) from peptides_class_2_alleles_II.join(input_vcf_neoepitope_II, by:[0,1], remainder:true)

nextflow.config

@@ -94,7 +94,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/mhcquant:1.5'
+process.container = 'nfcore/mhcquant:1.5.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -162,7 +162,7 @@ manifest {
   description = 'Identify and quantify peptides from mass spectrometry raw data'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.5'
+  version = '1.5.1'
 }
 
 // Function to ensure that resource requirements don't go beyond